The system peaks that often appear on electropherograms in anion separation by CE with indirect spectrophotometric detection, negative voltage polarity and cathodic EOF are studied. The system peaks are shown to correspond to the zones with the changed concentration of the BGE constituents; they appear while the zone of each analyte anion passes through the outlet end of the capillary and are transported to the detector by EOF. An equation is suggested for predicting migration times of the system peaks with an error of 1%. The ratios of the system peak area to the analyte peak area are found to amount to 20%. It is shown that it is possible to avoid overlapping of the system peaks and analyte peaks by controlling the EOF velocity owing to hydrodynamic pressure. Using the mathematical simulation of CE shows that the system peaks and baseline shift can result from changing the transference numbers of the BGE ions and analyte ions at the capillary edge. The cases when the system peak may be incorrectly identified as the peak of analyte ion are considered. In order to avoid such errors, some practical recommendations are given.